/*
    * Licensed to the Apache Software Foundation (ASF) under one   *
    * or more contributor license agreements.  See the NOTICE file *
    * distributed with this work for additional information        *
    * regarding copyright ownership.  The ASF licenses this file   *
    * to you under the Apache License, Version 2.0 (the            *
    * "License"); you may not use this file except in compliance   *
    * with the License.  You may obtain a copy of the License at   *
    *                                                              *
   *   http://www.apache.org/licenses/LICENSE-2.0                 *
   *                                                              *
   * Unless required by applicable law or agreed to in writing,   *
   * software distributed under the License is distributed on an  *
   * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY       *
   * KIND, either express or implied.  See the License for the    *
   * specific language governing permissions and limitations      *
   * under the License.                                           *
   */
  package org.apache.rat.commandline;
  
  import java.io.File;
  import java.io.IOException;
  import java.io.InputStream;
  import java.lang.reflect.Array;
  import java.nio.charset.StandardCharsets;
  import java.nio.file.Files;
  import java.util.ArrayList;
  import java.util.Arrays;
  import java.util.List;
  import java.util.function.BiConsumer;
  import java.util.function.Predicate;
  
  import org.apache.commons.cli.AlreadySelectedException;
  import org.apache.commons.cli.CommandLine;
  import org.apache.commons.cli.DeprecatedAttributes;
  import org.apache.commons.cli.Option;
  import org.apache.commons.cli.OptionGroup;
  import org.apache.commons.cli.Options;
  import org.apache.commons.cli.ParseException;
  import org.apache.commons.io.IOUtils;
  import org.apache.commons.lang3.tuple.Pair;
  import org.apache.rat.ConfigurationException;
  import org.apache.rat.Defaults;
  import org.apache.rat.ImplementationException;
  import org.apache.rat.ReportConfiguration;
  import org.apache.rat.config.AddLicenseHeaders;
  import org.apache.rat.config.exclusion.ExclusionUtils;
  import org.apache.rat.config.exclusion.StandardCollection;
  import org.apache.rat.document.DocumentName;
  import org.apache.rat.document.DocumentNameMatcher;
  import org.apache.rat.license.LicenseSetFactory;
  import org.apache.rat.report.claim.ClaimStatistic.Counter;
  import org.apache.rat.ui.UIOptionCollection;
  import org.apache.rat.utils.DefaultLog;
  import org.apache.rat.utils.Log;
  
  import static java.lang.String.format;
  
  /**
   * An enumeration of options that are recommended across all UIs. A UI may not implement some options if they are unsupportable
   * within the UI.
   * Each Arg contains:
   * <ul>
   *      <li>An OptionGroup that contains the individual options that all resolve to the same option.
   * This allows us to deprecate options as we move forward in development.</li>
   * <li>A {@code BiConsumer<ArgumentContext, Option>} that defines the process to configure the option in
   * the {@code ArgumentContext.configuration}.</li>
   * </ul>
   */
  public enum Arg {
      ///////////////////////// EDIT OPTIONS
      /**
       * Defines options to add copyright to files.
       */
      EDIT_COPYRIGHT(new OptionGroup()
              .addOption(Option.builder("c")
                      .longOpt("copyright").hasArg()
                      .deprecated(DeprecatedAttributes.builder().setForRemoval(true).setSince("0.17")
                              .setDescription(StdMsgs.useMsg("--edit-copyright")).get())
                      .desc("The copyright message to use in the license headers.")
                      .build())
              .addOption(Option.builder().longOpt("edit-copyright").hasArg()
                      .desc("The copyright message to use in the license headers. Usually in the form of \"Copyright 2008 Foo\".  "
                              + "Only valid with --edit-license")
                      .build()),
      Arg::doNotExecute
      ),
  
      /**
       * Causes file updates to overwrite existing files.
       */
      EDIT_OVERWRITE(new OptionGroup()
              .addOption(Option.builder("f").longOpt("force")
                      .deprecated(DeprecatedAttributes.builder().setForRemoval(true).setSince("0.17")
                              .setDescription(StdMsgs.useMsg("--edit-overwrite")).get())
                      .desc("Forces any changes in files to be written directly to the source files so that new files are not created.")
                      .build())
              .addOption(Option.builder().longOpt("edit-overwrite")
                      .desc("Forces any changes in files to be written directly to the source files so that new files are not created. "
                             + "Only valid with --edit-license.")
                     .build()),
             Arg::doNotExecute
     ),
 
     /**
      * Defines options to add licenses to files.
      */
     EDIT_ADD(new OptionGroup()
             .addOption(Option.builder("a")
                     .deprecated(DeprecatedAttributes.builder().setForRemoval(true).setSince("0.17")
                             .setDescription(StdMsgs.useMsg("--edit-license")).get())
                     .build())
             .addOption(Option.builder("A").longOpt("addLicense")
                     .deprecated(DeprecatedAttributes.builder().setForRemoval(true).setSince("0.17")
                             .setDescription(StdMsgs.useMsg("--edit-license")).get())
                     .desc("Add the Apache-2.0 license header to any file with an unknown license that is not in the exclusion list.")
                     .build())
             .addOption(Option.builder().longOpt("edit-license").desc(
                     "Add the Apache-2.0 license header to any file with an unknown license that is not in the exclusion list. "
                             + "By default new files will be created with the license header, "
                             + "to force the modification of existing files use the --edit-overwrite option.").build()
             ),
             Arg::doNotExecute
     ),
 
     //////////////////////////// CONFIGURATION OPTIONS
     /**
      * Group of options that read a configuration file.
      */
     CONFIGURATION(new OptionGroup()
             .addOption(Option.builder().longOpt("config").hasArgs().argName("File")
                     .desc("File names for system configuration.")
                     .converter(Converters.FILE_CONVERTER)
                     .type(DocumentName.class)
                     .build())
             .addOption(Option.builder().longOpt("licenses").hasArgs().argName("File")
                     .desc("File names for system configuration.")
                     .deprecated(DeprecatedAttributes.builder().setSince("0.17").setForRemoval(true).setDescription(StdMsgs.useMsg("--config")).get())
                     .converter(Converters.FILE_CONVERTER)
                     .type(DocumentName.class)
                     .build()),
             Arg::doNotExecute
     ),
 
     /**
      * Group of options that skip the default configuration file.
      */
     CONFIGURATION_NO_DEFAULTS(new OptionGroup()
             .addOption(Option.builder().longOpt("configuration-no-defaults")
                     .desc("Ignore default configuration.").build())
             .addOption(Option.builder().longOpt("no-default-licenses")
                     .deprecated(DeprecatedAttributes.builder()
                             .setSince("0.17")
                             .setForRemoval(true)
                             .setDescription(StdMsgs.useMsg("--configuration-no-defaults")).get())
                     .desc("Ignore default configuration.")
                     .build()),
             Arg::doNotExecute
     ),
 
     /**
      * Option that adds approved licenses to the list.
      */
     LICENSES_APPROVED(new OptionGroup().addOption(Option.builder().longOpt("licenses-approved").hasArg().argName("LicenseID")
             .desc("A comma separated list of approved License IDs. These licenses will be added to the list of approved licenses.")
             .converter(Converters.TEXT_LIST_CONVERTER)
             .type(String[].class)
             .build()),
             (context, selected) ->
                 context.getConfiguration().addApprovedLicenseIds(processArrayArg(context, selected))
     ),
 
     /**
      * Option that adds approved licenses from a file.
      */
     LICENSES_APPROVED_FILE(new OptionGroup().addOption(Option.builder().longOpt("licenses-approved-file").hasArg().argName("File")
             .desc("Name of file containing comma separated lists of approved License IDs.")
             .converter(Converters.FILE_CONVERTER)
             .type(DocumentName.class)
             .build()),
             (context, selected) ->
                     context.getConfiguration().addApprovedLicenseIds(processArrayFile(context, selected))),
 
     /**
      * Option that specifies approved license families.
      */
     FAMILIES_APPROVED(new OptionGroup().addOption(Option.builder().longOpt("license-families-approved").hasArg().argName("FamilyID")
             .desc("A comma separated list of approved license family IDs. These license families will be added to the list of approved license families.")
             .converter(Converters.TEXT_LIST_CONVERTER)
             .type(String[].class)
             .build()),
             (context, selected) -> context.getConfiguration().addApprovedLicenseCategories(processArrayArg(context, selected))),
 
     /**
      * Option that specifies approved license families from a file.
      */
     FAMILIES_APPROVED_FILE(new OptionGroup().addOption(Option.builder().longOpt("license-families-approved-file").hasArg().argName("File")
             .desc("Name of file containing comma separated lists of approved family IDs.")
             .converter(Converters.FILE_CONVERTER)
             .type(DocumentName.class)
             .build()),
             (context, selected) -> context.getConfiguration().addApprovedLicenseCategories(processArrayFile(context, selected))
     ),
 
     /**
      * Option to remove licenses from the approved list.
      */
     LICENSES_DENIED(new OptionGroup().addOption(Option.builder().longOpt("licenses-denied").hasArg().argName("LicenseID")
             .desc("A comma separated list of denied License IDs. " +
                     "These licenses will be removed from the list of approved licenses. " +
                     "Once licenses are removed they can not be added back.")
             .converter(Converters.TEXT_LIST_CONVERTER)
             .type(String[].class)
             .build()),
             (context, selected) -> context.getConfiguration().removeApprovedLicenseIds(processArrayArg(context, selected))),
 
     /**
      * Option to read a file licenses to be removed from the approved list.
      */
     LICENSES_DENIED_FILE(new OptionGroup().addOption(Option.builder().longOpt("licenses-denied-file")
             .hasArg().argName("File").type(File.class)
             .converter(Converters.FILE_CONVERTER)
             .desc("Name of file containing comma separated lists of the denied license IDs. " +
                     "These licenses will be removed from the list of approved licenses. " +
                     "Once licenses are removed they can not be added back.")
             .build()),
             (context, selected) -> context.getConfiguration().removeApprovedLicenseIds(processArrayFile(context, selected))),
 
     /**
      * Option to list license families to remove from the approved list.
      */
     FAMILIES_DENIED(new OptionGroup().addOption(Option.builder().longOpt("license-families-denied")
             .hasArg().argName("FamilyID")
             .desc("A comma separated list of denied License family IDs. " +
                     "These license families will be removed from the list of approved licenses. " +
                     "Once license families are removed they can not be added back.")
             .converter(Converters.TEXT_LIST_CONVERTER)
             .type(String[].class)
             .build()),
             (context, selected) -> context.getConfiguration().removeApprovedLicenseCategories(processArrayArg(context, selected))),
 
     /**
      * Option to read a list of license families to remove from the approved list.
      */
     FAMILIES_DENIED_FILE(new OptionGroup().addOption(Option.builder().longOpt("license-families-denied-file").hasArg().argName("File")
             .desc("Name of file containing comma separated lists of denied license IDs. " +
                     "These license families will be removed from the list of approved licenses. " +
                     "Once license families are removed they can not be added back.")
             .type(DocumentName.class)
             .converter(Converters.FILE_CONVERTER)
             .build()),
             (context, selected) -> context.getConfiguration().removeApprovedLicenseCategories(processArrayFile(context, selected))),
 
     /**
      * Option to specify an acceptable number of various counters.
      */
     COUNTER_MAX(new OptionGroup().addOption(Option.builder().longOpt("counter-max").hasArgs().argName("CounterPattern")
             .desc("The acceptable maximum number for the specified counter. A value of '-1' specifies an unlimited number.")
             .converter(Converters.COUNTER_CONVERTER)
             .type(Pair.class)
             .build()),
             (context, selected) -> {
                 for (String arg : context.getCommandLine().getOptionValues(selected)) {
                     Pair<Counter, Integer> pair = Converters.COUNTER_CONVERTER.apply(arg);
                     int limit = pair.getValue();
                     context.getConfiguration().getClaimValidator().setMax(pair.getKey(), limit < 0 ? Integer.MAX_VALUE : limit);
                 }
             }),
 
     /**
      * Option to specify an acceptable number of various counters.
      */
     COUNTER_MIN(new OptionGroup().addOption(Option.builder().longOpt("counter-min").hasArgs().argName("CounterPattern")
             .desc("The minimum number for the specified counter.")
             .converter(Converters.COUNTER_CONVERTER)
             .type(Pair.class)
             .build()),
             (context, selected) -> {
                 for (String arg : context.getCommandLine().getOptionValues(selected)) {
                     Pair<Counter, Integer> pair = Converters.COUNTER_CONVERTER.apply(arg);
                     context.getConfiguration().getClaimValidator().setMin(pair.getKey(), pair.getValue());
                 }
             }),
 
 ////////////////// INPUT OPTIONS
     /**
      * Reads files to test from a file.
      */
     SOURCE(new OptionGroup()
             .addOption(Option.builder().longOpt("input-source").hasArgs().argName("File")
                     .desc("A file containing file names to process. " +
                             "File names must use linux directory separator ('/') or none at all. " +
                             "File names that do not start with '/' are relative to the directory where the " +
                             "argument is located.")
                     .converter(Converters.FILE_CONVERTER)
                     .type(DocumentName.class)
                     .build()),
             (context, selected) -> {
                 DocumentName[] documentNames = getParsedOptionValues(selected, context.getCommandLine());
                 for (DocumentName documentName : documentNames) {
                     context.getConfiguration().addSource(documentName.asFile());
                 }
             }),
 
     /**
      * Excludes files by expression.
      */
     EXCLUDE(new OptionGroup()
             .addOption(Option.builder("e").longOpt("exclude").hasArgs().argName("Expression")
                     .deprecated(DeprecatedAttributes.builder().setForRemoval(true).setSince("0.17")
                             .setDescription(StdMsgs.useMsg("--input-exclude")).get())
                     .desc("Excludes files matching <Expression>.")
                     .build())
             .addOption(Option.builder().longOpt("input-exclude").hasArgs().argName("Expression")
                     .desc("Excludes files matching <Expression>.")
                     .build()),
             (context, selected) -> {
                 String[] excludes = context.getCommandLine().getOptionValues(selected);
                 if (excludes != null) {
                     context.getConfiguration().addExcludedPatterns(Arrays.asList(excludes));
                 }
             }),
 
     /**
      * Excludes files based on the contents of a file.
      */
     EXCLUDE_FILE(new OptionGroup()
             .addOption(Option.builder("E").longOpt("exclude-file")
                     .argName("File").hasArg().type(File.class)
                     .converter(Converters.FILE_CONVERTER)
                     .deprecated(DeprecatedAttributes.builder().setForRemoval(true).setSince("0.17")
                             .setDescription(StdMsgs.useMsg("--input-exclude-file")).get())
                     .desc("Reads <Expression> entries from a file. Entries will be excluded from processing.")
                     .build())
             .addOption(Option.builder().longOpt("input-exclude-file")
                     .argName("File").hasArg().type(File.class)
                     .converter(Converters.FILE_CONVERTER)
                     .desc("Reads <Expression> entries from a file. Entries will be excluded from processing.")
                     .build()),
             (context, selected) -> {
                 try {
                     DocumentName excludeFileName = context.getCommandLine().getParsedOptionValue(selected);
                     if (excludeFileName != null) {
                         context.getConfiguration().addExcludedPatterns(ExclusionUtils.asIterable(excludeFileName.asFile(), "#"));
                     }
                 } catch (Exception e) {
                     throw ConfigurationException.from(e);
                 }
             }),
     /**
      * Excludes files based on standard groupings.
      */
     EXCLUDE_STD(new OptionGroup()
             .addOption(Option.builder().longOpt("input-exclude-std").argName("StandardCollection")
                     .hasArgs().converter(s -> StandardCollection.valueOf(s.toUpperCase()))
                     .desc("Excludes files defined in standard collections based on commonly occurring groups. " +
                             "Excludes any path matcher actions but DOES NOT exclude any file processor actions.")
                     .type(StandardCollection.class)
                     .build()),
             (context, selected) -> {
                 for (String s : context.getCommandLine().getOptionValues(selected)) {
                     context.getConfiguration().addExcludedCollection(StandardCollection.valueOf(s));
                 }
             }),
 
     /**
      * Excludes files if they are smaller than the given threshold.
      */
     EXCLUDE_SIZE(new OptionGroup()
             .addOption(Option.builder().longOpt("input-exclude-size").argName("Integer")
                     .hasArg().type(Integer.class)
                     .desc("Excludes files with sizes less than the number of bytes specified.")
                     .build()),
             (context, selected) -> {
                 try {
                     final int maxSize = context.getCommandLine().getParsedOptionValue(selected);
                     DocumentNameMatcher matcher = new DocumentNameMatcher(String.format("File size < %s bytes", maxSize),
                             (Predicate<DocumentName>) documentName -> {
                                 File f = new File(documentName.getName());
                                 return f.isFile() && f.length() < maxSize;
                             });
                     context.getConfiguration().addExcludedMatcher(matcher);
                 } catch (Exception e) {
                     throw ConfigurationException.from(e);
                 }
             }),
     /**
      * Excludes files by expression.
      */
     INCLUDE(new OptionGroup()
             .addOption(Option.builder().longOpt("input-include").hasArgs().argName("Expression")
                     .desc("Includes files matching <Expression>. Will override excluded files.")
                     .build())
             .addOption(Option.builder().longOpt("include").hasArgs().argName("Expression")
                     .desc("Includes files matching <Expression>. Will override excluded files.")
                     .deprecated(DeprecatedAttributes.builder().setForRemoval(true).setSince("0.17")
                             .setDescription(StdMsgs.useMsg("--input-include")).get())
                     .build()),
             (context, selected) -> {
                 String[] includes = context.getCommandLine().getOptionValues(selected);
                 if (includes != null) {
                     context.getConfiguration().addIncludedPatterns(Arrays.asList(includes));
                 }
             }),
 
     /**
      * Includes files based on the contents of a file.
      */
     INCLUDE_FILE(new OptionGroup()
             .addOption(Option.builder().longOpt("input-include-file")
                     .argName("File").hasArg().type(File.class)
                     .converter(Converters.FILE_CONVERTER)
                     .desc("Reads <Expression> entries from a file. Entries will override excluded files.")
                     .build())
             .addOption(Option.builder().longOpt("includes-file")
                     .argName("File").hasArg().type(File.class)
                     .converter(Converters.FILE_CONVERTER)
                     .desc("Reads <Expression> entries from a file. Entries will override excluded files.")
                     .deprecated(DeprecatedAttributes.builder().setForRemoval(true).setSince("0.17")
                             .setDescription(StdMsgs.useMsg("--input-include-file")).get())
                     .build()),
             (context, selected) -> {
                 try {
                     DocumentName includeFileName = context.getCommandLine().getParsedOptionValue(selected);
                     if (includeFileName != null) {
                         context.getConfiguration().addIncludedPatterns(ExclusionUtils.asIterable(includeFileName.asFile(), "#"));
                     }
                 } catch (Exception e) {
                     throw ConfigurationException.from(e);
                 }
             }),
 
     /**
      * Includes files based on standard groups.
      */
     INCLUDE_STD(new OptionGroup()
             .addOption(Option.builder().longOpt("input-include-std").argName("StandardCollection")
                     .hasArgs().converter(s -> StandardCollection.valueOf(s.toUpperCase()))
                     .desc("Includes files defined in standard collections based on commonly occurring groups. " +
                             "Includes any path matcher actions but DOES NOT include any file processor actions.")
                     .type(StandardCollection.class)
                     .build())
             .addOption(Option.builder().longOpt("scan-hidden-directories")
                     .desc("Scans hidden directories.")
                     .deprecated(DeprecatedAttributes.builder().setForRemoval(true).setSince("0.17")
                             .setDescription(StdMsgs.useMsg("--input-include-std with 'HIDDEN_DIR' argument")).get()).build()
             ),
             (context, selected) -> {
                 // display deprecation log if needed.
                 if (context.getCommandLine().hasOption("scan-hidden-directories")) {
                     context.getConfiguration().addIncludedCollection(StandardCollection.HIDDEN_DIR);
                 } else {
                     for (String s : context.getCommandLine().getOptionValues(selected)) {
                         context.getConfiguration().addIncludedCollection(StandardCollection.valueOf(s));
                     }
                 }
             }),
 
     /**
      * Excludes files based on SCM exclusion file processing.
      */
     EXCLUDE_PARSE_SCM(new OptionGroup()
             .addOption(Option.builder().longOpt("input-exclude-parsed-scm")
                     .argName("StandardCollection")
                     .hasArgs().converter(s -> StandardCollection.valueOf(s.toUpperCase()))
                     .desc("Parse SCM based exclusion files to exclude specified files and directories. " +
                             "This action can apply to any standard collection that implements a file processor.")
                     .type(StandardCollection.class)
                     .build()),
             (context, selected) -> {
                 StandardCollection[] collections = getParsedOptionValues(selected, context.getCommandLine());
                 final ReportConfiguration configuration = context.getConfiguration();
                 for (StandardCollection collection : collections) {
                     if (collection == StandardCollection.ALL) {
                         Arrays.asList(StandardCollection.values()).forEach(configuration::addExcludedFileProcessor);
                         Arrays.asList(StandardCollection.values()).forEach(configuration::addExcludedCollection);
                     } else {
                         configuration.addExcludedFileProcessor(collection);
                         configuration.addExcludedCollection(collection);
                     }
                 }
             }),
 
     /**
      * Stop processing an input stream and declare an input file.
      */
     DIR(new OptionGroup().addOption(Option.builder().option("d").longOpt("dir").hasArg()
             .type(File.class)
             .desc("Used to indicate end of list when using options that take multiple arguments.").argName("DirOrArchive")
             .deprecated(DeprecatedAttributes.builder().setForRemoval(true).setSince("0.17")
                     .setDescription("Use the standard '--' to signal the end of arguments.").get()).build()),
             Arg::doNotExecute
     ),
 
     /////////////// OUTPUT OPTIONS
     /**
      * Defines the stylesheet to use.
      */
     OUTPUT_STYLE(new OptionGroup()
             .addOption(Option.builder().longOpt("output-style").hasArg().argName("StyleSheet")
                     .desc("XSLT stylesheet to use when creating the report. "
                             + "Either an external xsl file may be specified or one of the internal named sheets.")
                     .build())
             .addOption(Option.builder("s").longOpt("stylesheet").hasArg().argName("StyleSheet")
                     .deprecated(DeprecatedAttributes.builder().setSince("0.17").setForRemoval(true).setDescription(StdMsgs.useMsg("--output-style")).get())
                     .desc("XSLT stylesheet to use when creating the report.")
                     .build())
             .addOption(Option.builder("x").longOpt("xml")
                     .deprecated(DeprecatedAttributes.builder()
                             .setSince("0.17")
                             .setForRemoval(true)
                             .setDescription(StdMsgs.useMsg("--output-style with the 'xml' argument")).get())
                     .desc("forces XML output rather than the textual report.")
                     .build()),
             (context, selected) -> {
                 String key = selected.getKey(); // is not null due to above isSelected()-call
                 if ("x".equals(key)) {
                     // display deprecated message.
                     context.getCommandLine().hasOption("x");
                     context.getConfiguration().setStyleSheet(StyleSheets.getStyleSheet("xml"));
                 } else {
                     String[] style = context.getCommandLine().getOptionValues(selected);
                     if (style.length != 1) {
                         DefaultLog.getInstance().error("Please specify a single stylesheet");
                         throw new ConfigurationException("Please specify a single stylesheet");
                     }
                     context.getConfiguration().setStyleSheet(StyleSheets.getStyleSheet(style[0]));
                 }
             }),
 
     /**
      * Specifies the license definitions that should be included in the output.
      */
     OUTPUT_LICENSES(new OptionGroup()
             .addOption(Option.builder().longOpt("output-licenses").hasArg().argName("LicenseFilter")
                     .desc("List the defined licenses.")
                     .converter(s -> LicenseSetFactory.LicenseFilter.valueOf(s.toUpperCase()))
                     .build())
             .addOption(Option.builder().longOpt("list-licenses").hasArg().argName("LicenseFilter")
                     .desc("List the defined licenses.")
                     .converter(s -> LicenseSetFactory.LicenseFilter.valueOf(s.toUpperCase()))
                     .deprecated(DeprecatedAttributes.builder().setSince("0.17").setForRemoval(true).setDescription(StdMsgs.useMsg("--output-licenses")).get())
                     .build()),
             (context, selected) -> {
                 try {
                     context.getConfiguration().listLicenses(context.getCommandLine().getParsedOptionValue(selected));
                 } catch (ParseException e) {
                     context.logParseException(e, selected, Defaults.LIST_LICENSES);
                 }
             }),
 
     /**
      * Specifies the license families that should be included in the output.
      */
     OUTPUT_FAMILIES(new OptionGroup()
             .addOption(Option.builder().longOpt("output-families").hasArg().argName("LicenseFilter")
                     .desc("List the defined license families.")
                     .converter(s -> LicenseSetFactory.LicenseFilter.valueOf(s.toUpperCase()))
                     .build())
             .addOption(Option.builder().longOpt("list-families").hasArg().argName("LicenseFilter")
                     .desc("List the defined license families.")
                     .converter(s -> LicenseSetFactory.LicenseFilter.valueOf(s.toUpperCase()))
                     .deprecated(DeprecatedAttributes.builder().setSince("0.17").setForRemoval(true).setDescription(StdMsgs.useMsg("--output-families")).get())
                     .build()),
             (context, selected) -> {
                 try {
                     context.getConfiguration().listFamilies(context.getCommandLine().getParsedOptionValue(selected));
                 } catch (ParseException e) {
                     context.logParseException(e, selected, Defaults.LIST_FAMILIES);
                 }
             }),
 
     /**
      * Specifies the log level to log messages at.
      */
     LOG_LEVEL(new OptionGroup().addOption(Option.builder().longOpt("log-level")
             .hasArg().argName("LogLevel")
             .desc("Sets the log level.")
             .converter(s -> Log.Level.valueOf(s.toUpperCase()))
             .build()),
             (context, selected) -> {
                 Log dLog = DefaultLog.getInstance();
                 try {
                     dLog.setLevel(context.getCommandLine().getParsedOptionValue(selected));
                 } catch (ParseException e) {
                     logParseException(DefaultLog.getInstance(), e, selected, context.getCommandLine(), dLog.getLevel());
                 }
             }),
 
     /**
      * Specifies that the run should not perform any updates to files.
      */
     DRY_RUN(new OptionGroup().addOption(Option.builder().longOpt("dry-run")
             .desc("If set do not update the files but generate the reports.")
             .build()),
             (context, selected) ->
                     context.getConfiguration().setDryRun(true)
     ),
 
     /**
      * Specifies where the output should be written.
      */
     OUTPUT_FILE(new OptionGroup()
             .addOption(Option.builder().option("o").longOpt("out").hasArg().argName("File")
                     .desc("Define the output file where to write a report to.")
                     .deprecated(DeprecatedAttributes.builder().setSince("0.17").setForRemoval(true).setDescription(StdMsgs.useMsg("--output-file")).get())
                     .type(DocumentName.class)
                     .converter(Converters.FILE_CONVERTER)
                     .build())
             .addOption(Option.builder().longOpt("output-file").hasArg().argName("File")
                     .desc("Define the output file where to write a report to.")
                     .type(DocumentName.class)
                     .converter(Converters.FILE_CONVERTER)
                     .build()),
             (context, selected) -> {
                 try {
                     DocumentName documentName = context.getCommandLine().getParsedOptionValue(selected);
                     File document = documentName.asFile();
                     File parent = document.getParentFile();
                     if (!parent.mkdirs() && !parent.isDirectory()) {
                         DefaultLog.getInstance().error("Could not create report parent directory " + documentName);
                     }
                     context.getConfiguration().setOut(document);
                 } catch (ParseException e) {
                     // we write to system out by default.
                     context.logParseException(e, selected, "System.out");
                     context.getConfiguration().setOut(ReportConfiguration.SYSTEM_OUT);
                 }
             }),
 
     /**
      * Specifies the level of reporting detail for archive files.
      */
     OUTPUT_ARCHIVE(new OptionGroup()
             .addOption(Option.builder().longOpt("output-archive").hasArg().argName("ProcessingType")
                     .desc("Specifies the level of detail in ARCHIVE file reporting.")
                     .converter(s -> ReportConfiguration.Processing.valueOf(s.toUpperCase()))
                     .build()),
             (context, selected) -> {
                 try {
                     context.getConfiguration().setArchiveProcessing(context.getCommandLine().getParsedOptionValue(selected));
                 } catch (ParseException e) {
                     context.logParseException(e, selected, Defaults.ARCHIVE_PROCESSING);
                 }
             }
     ),
 
     /**
      * Specifies the level of reporting detail for standard files.
      */
     OUTPUT_STANDARD(new OptionGroup()
             .addOption(Option.builder().longOpt("output-standard").hasArg().argName("ProcessingType")
                     .desc("Specifies the level of detail in STANDARD file reporting.")
                     .converter(s -> ReportConfiguration.Processing.valueOf(s.toUpperCase()))
                     .build()),
             (context, selected) -> {
                 try {
                     context.getConfiguration().setStandardProcessing(context.getCommandLine().getParsedOptionValue(selected));
                 } catch (ParseException e) {
                     context.logParseException(e, selected, Defaults.STANDARD_PROCESSING);
                 }
             }),
 
     /**
      * Provide license definition listing of registered licenses.
      */
     HELP_LICENSES(new OptionGroup()
             .addOption(Option.builder().longOpt("help-licenses") //
                     .desc("Print information about registered licenses.").build()),
             Arg::doNotExecute
     );
 
     /**
      * The option group for the argument.
      */
     private final OptionGroup group;
 
     /**
      * The BiConsumer to apply the option to update the state of the context.configuration.
      */
     private final BiConsumer<ArgumentContext, Option> process;
 
     /**
      * This method is used for an implementation marker. The options use this as the test process should be handled before
      * the standard processing. For example, EDIT_COPYRIGHT is only valid if EDIT_ADD is specified. The processes that handle EDIT_ADD
      * and EDIT_COPYRIGHT do not call the execute method as they have to make extra calls to display deprecated messages and otherwise
      * properly execute. If somehow, a UI attempts to execute them the UI testing should fail. This method ensures that happens when it
      * is specified as the process for the option.
      * @param context the current argument context.
      * @param selected the selected option.
      */
     private static void doNotExecute(final ArgumentContext context, final Option selected) {
         throw new ImplementationException(String.format("'%s' should not be executed directly", selected));
     }
 
     /**
      * Creates an Arg from an Option group.
      *
      * @param group The option group.
      * @param process The BiConsumer that executes the argument. Generally these processes apply the argument to the configuration or
      *                other component of the ArgumentContext.
      */
     Arg(final OptionGroup group, final BiConsumer<ArgumentContext, Option> process) {
         this.group = group;
         this.process = process;
     }
 
     /**
      * Executes the process associated with this Arg if the collection has an Option from this group selected.
      * @param context the ArgumentContext that is being processed.
      * @param optionCollection the OptionCollection that is available.
      */
     private void execute(final ArgumentContext context, final UIOptionCollection<?> optionCollection) {
         optionCollection.getSelected(this)
                 .ifPresent(selected -> this.process.accept(context, selected));
     }
 
     /**
      * Determines if all the options have been removed from this argument.
      *
      * @return {@code true} if all the options have been removed from this argument.
      */
     public boolean isEmpty() {
         return this.group().getOptions().isEmpty();
     }
 
     /**
      * Finds the element associated with the key within the element group.
      *
      * @param key the key to search for.
      * @return the matching Option.
      * @throws IllegalArgumentException if the key can not be found.
      */
     public Option find(final String key) {
         for (Option result : group.getOptions()) {
             if (key.equals(result.getKey()) || key.equals(result.getLongOpt())) {
                 return result;
             }
         }
         throw new IllegalArgumentException("Can not find " + key);
     }
 
     /**
      * Gets the group for this arg.
      *
      * @return the option group for this arg.
      */
     public OptionGroup group() {
         return group;
     }
 
     /**
      * Returns the first non-deprecated option from the group.
      *
      * @return the first non-deprecated option or, if no non-deprecated option is available, the first option.
      */
     public Option option() {
         Option first = null;
         for (Option result : group.getOptions()) {
             if (first == null) {
                 first = result;
             }
             if (!result.isDeprecated()) {
                 return result;
             }
         }
         return first;
     }
 
     /**
      * Gets the full set of options.
      *
      * @return the full set of options for this Arg.
      */
     public static Options getOptions() {
         Options options = new Options();
         for (Arg arg : Arg.values()) {
             options.addOptionGroup(arg.group);
         }
         return options;
     }
 
     /**
      * Processes the edit arguments.
      *
      * @param context the context to work with.
      */
     private static void processEditArgs(final ArgumentContext context, final UIOptionCollection<?> optionCollection) {
         optionCollection.getSelected(EDIT_ADD).ifPresent(option -> {
             // prints deprecation
             context.getCommandLine().hasOption(option);
             boolean force = optionCollection.isSelected(EDIT_OVERWRITE);
             if (force) {
                 // prints deprecation
                 optionCollection.getSelected(EDIT_OVERWRITE).ifPresent(context.getCommandLine()::hasOption);
             }
             context.getConfiguration().setAddLicenseHeaders(force ? AddLicenseHeaders.FORCED : AddLicenseHeaders.TRUE);
             optionCollection.getSelected(EDIT_COPYRIGHT).
                     ifPresent(editOption -> context.getConfiguration().setCopyrightMessage(context.getCommandLine().getOptionValue(editOption)));
         });
     }
 
     /**
      * Gets the list of Strings that are arguments for the option.
      * @param context the ArgumentContext containing the command line.
      * @param selected the selected option.
      * @return the list of Strings that are arguments.
      */
     private static List<String> processArrayArg(final ArgumentContext context, final Option selected) {
         try {
             return Arrays.asList(context.getCommandLine().getParsedOptionValue(selected));
         } catch (ParseException e) {
             throw new ConfigurationException(e);
         }
     }
 
     /**
      * Parses the option as a file.
      * @param context the Argument context that provides the command line.
      * @param selected the selected option.
      * @return Option as a file.
      */
     private static File commandLineFile(final ArgumentContext context, final Option selected) throws ParseException {
         DocumentName documentName = context.getCommandLine().getParsedOptionValue(selected);
         return documentName.asFile();
     }
 
     /**
      * Parses lines with comma separated tokens from a file and returns the entire collection of tokens as a list of strings.
      * @param context the Argument context that provides the command line.
      * @param selected the selected option.
      * @return the list of strings parsed from the file.
      */
     private static List<String> processArrayFile(final ArgumentContext context, final Option selected) {
         List<String> result = new ArrayList<>();
         try (InputStream in = Files.newInputStream(commandLineFile(context, selected)
                 .toPath())) {
             for (String line : IOUtils.readLines(in, StandardCharsets.UTF_8)) {
                 String[] ids = Converters.TEXT_LIST_CONVERTER.apply(line);
                 result.addAll(Arrays.asList(ids));
             }
             return result;
         } catch (IOException e) {
             throw new ConfigurationException(e);
 
         } catch (ParseException e) {
             throw ConfigurationException.from(e);
         }
     }
 
     /**
      * Processes the configuration options.
      *
      * @param context the context to process.
      * @throws ConfigurationException if configuration files can not be read.
      */
     private static void processConfigurationArgs(final ArgumentContext context, final UIOptionCollection<?> optionCollection) throws ConfigurationException {
 
         Defaults.Builder defaultBuilder = Defaults.builder();
 
         optionCollection.getSelected(CONFIGURATION).ifPresent(
                 selected -> {
                     DocumentName[] documentNames = getParsedOptionValues(selected, context.getCommandLine());
                     for (DocumentName documentName : documentNames) {
                         defaultBuilder.add(documentName.asFile());
                     }
                 });
         optionCollection.getSelected(CONFIGURATION_NO_DEFAULTS).ifPresent(selected -> {
             // display deprecation log if needed.
             context.getCommandLine().hasOption(selected);
             defaultBuilder.noDefault();
         });
         context.getConfiguration().setFrom(defaultBuilder.build());
 
         for (Arg arg : List.of(FAMILIES_APPROVED, FAMILIES_APPROVED_FILE, FAMILIES_DENIED, FAMILIES_DENIED_FILE,
                 LICENSES_APPROVED, LICENSES_APPROVED_FILE, LICENSES_DENIED, LICENSES_DENIED_FILE,
                 COUNTER_MAX, COUNTER_MIN)) {
             arg.execute(context, optionCollection);
         }
     }
 
     /**
      * Process the input setup.
      *
      * @param context the context to work in.
      * @throws ConfigurationException if an exclude file can not be read.
      */
     private static void processInputArgs(final ArgumentContext context, final UIOptionCollection<?> optionCollection) throws ConfigurationException {
         for (Arg arg : List.of(SOURCE, EXCLUDE, EXCLUDE_FILE, EXCLUDE_STD, EXCLUDE_PARSE_SCM, EXCLUDE_SIZE,
                 INCLUDE, INCLUDE_FILE, INCLUDE_STD)) {
             arg.execute(context, optionCollection);
         }
     }
 
     /**
      * Logs a ParseException as a warning.
      *
      * @param log the Log to write to
      * @param exception the parse exception to log
      * @param opt the option being processed
      * @param cl the command line being processed
      * @param defaultValue The default value the option is being set to.
      */
     private static void logParseException(final Log log, final ParseException exception, final Option opt, final CommandLine cl, final Object defaultValue) {
         log.warn(format("Invalid %s specified: %s ", opt.getOpt(), cl.getOptionValue(opt)));
         log.warn(format("%s set to: %s", opt.getOpt(), defaultValue));
         log.debug(exception);
     }
 
     /**
      * Process the log level setting.
      *
      * @param context The argument context
      */
     public static void processLogLevel(final ArgumentContext context, final UIOptionCollection<?> optionCollection) throws ConfigurationException {
         LOG_LEVEL.execute(context, optionCollection);
     }
 
     /**
      * Process the arguments.
      *
      * @param context the context in which to process the args.
      * @throws ConfigurationException on error
      */
     public static void processArgs(final ArgumentContext context, final UIOptionCollection<?> optionCollection) throws ConfigurationException {
         Converters.FILE_CONVERTER.setWorkingDirectory(context.getWorkingDirectory());
         processOutputArgs(context, optionCollection);
         processEditArgs(context, optionCollection);
         processInputArgs(context, optionCollection);
         processConfigurationArgs(context, optionCollection);
     }
 
     /**
      * Process the arguments that can be processed together.
      *
      * @param context the context in which to process the args.
      */
     private static void processOutputArgs(final ArgumentContext context, final UIOptionCollection<?> optionCollection) throws ConfigurationException {
         for (Arg arg : List.of(DRY_RUN, OUTPUT_FAMILIES, OUTPUT_LICENSES, OUTPUT_ARCHIVE, OUTPUT_STANDARD, OUTPUT_FILE, OUTPUT_STYLE)) {
             arg.execute(context, optionCollection);
         }
     }
 
     /**
      * Resets the groups in the Args so that they are unused and ready to detect the next set of arguments.
      */
     public static void reset() {
         for (Arg a : Arg.values()) {
             try {
                 a.group.setSelected(null);
             } catch (AlreadySelectedException e) {
                 throw new RuntimeException("Should not happen", e);
             }
         }
     }
 
     /**
      * Finds the Arg that contains an Option with the specified key.
      *
      * @param key the key for the Option to locate.
      * @return The Arg or {@code null} if no Arg is found.
      */
     public static Arg findArg(final String key) {
         if (key != null) {
             for (Arg arg : Arg.values()) {
                 for (Option candidate : arg.group.getOptions()) {
                     if (key.equals(candidate.getKey()) || key.equals(candidate.getLongOpt())) {
                         return arg;
                     }
                 }
             }
         }
         return null;
     }
 
     private static <T> T[] getParsedOptionValues(final Option selected, final CommandLine commandLine) {
         try {
             Class<? extends T> clazz = (Class<? extends T>) selected.getType();
             String[] values = commandLine.getOptionValues(selected);
             T[] result = (T[]) Array.newInstance(clazz, values.length);
             for (int i = 0; i < values.length; i++) {
                 result[i] = clazz.cast(selected.getConverter().apply(values[i]));
             }
             return result;
         } catch (Throwable t) {
             throw new ConfigurationException(format("'%s' converter for %s '%s' does not produce a class of type %s", selected,
                     selected.getKey(), selected.getConverter().getClass().getName(), selected.getType()), t);
         }
     }
 
     /**
      * Standard messages used in descriptions.
      */
     public static final class StdMsgs {
         private StdMsgs() {
             // do not instantiate
         }
 
         /**
          * Gets the standard "use instead" message for the specific name.
          *
          * @param name the name of the option to use instead.
          * @return combined "use instead" message.
          */
         public static String useMsg(final String name) {
             return format("Use %s instead.", name);
         }
     }
 }